Data from: SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar)

Atlantic salmon (Salmo salar) is one of the most extensively studied fish species in the world due to its significance in aquaculture, fisheries and ongoing conservation efforts to protect declining populations. Yet, limited genomic resources have hampered our understanding of genetic architecture in the species and the genetic basis of adaptation to the wide range of natural and artificial environments it occupies. In this paper, we describe the development of a medium density Atlantic salmon SNP-array based on Expressed Sequence Tags (ESTs) and genomic sequencing. The array was used in the most extensive assessment of population genetic structure performed to date in this species. A total of 6176 informative SNPs were successfully genotyped in 38 anadromous and freshwater wild populations distributed across the species natural range. Principal component analysis clearly differentiated European and North American populations, and within Europe, three major regional genetic groups were identified for the first time in a single analysis. We assessed the potential for the array to disentangle neutral and putative adaptive divergence of SNP allele frequencies across populations and among regional groups. In Europe, secondary contact zones were identified between major clusters where endogenous and exogenous barriers could be associated, rendering the interpretation of environmental influence on potentially adaptive divergence equivocal. A small number of markers highly divergent in allele frequencies (outliers) were observed between (multiple) freshwater and anadromous populations, between northern and southern latitudes, and when comparing Baltic populations to all others. We also discuss the potential future applications of the SNP-array for conservation, management and aquaculture.大西洋鲑（Atlantic salmon，学名Salmo salar）是全球被研究最为广泛的鱼类物种之一，因其在水产养殖、渔业及针对种群衰退的持续性保护工作中具有重要价值。然而，有限的基因组学资源阻碍了我们对该物种遗传架构以及其适应其所栖息的多样自然与人工环境的遗传基础的认知。本研究阐述了一款基于表达序列标签（Expressed Sequence Tags，ESTs）与基因组测序技术开发的中密度大西洋鲑单核苷酸多态性芯片（SNP-array）的构建过程。该芯片被应用于该物种迄今为止规模最大的种群遗传结构评估工作。研究共对分布于该物种自然分布范围内的38个溯河洄游型与淡水型野生种群的6176个信息性单核苷酸多态性位点（SNP）成功完成了基因分型。主成分分析（Principal Component Analysis，PCA）清晰区分了欧洲与北美种群，且在单次分析中首次于欧洲内部鉴定出三大区域性遗传类群。本研究评估了该芯片用于解析不同种群间及区域性类群间SNP等位基因频率的中性分化与推定适应性分化的潜力。在欧洲区域，主要遗传簇之间被鉴定存在次级接触区，该区域可能同时关联内源与外源生殖隔离障碍，这使得环境对潜在适应性分化的影响的解读变得模棱两可。研究还观察到少量等位基因频率差异显著的标记（即异常位点，outliers），分别出现在多组淡水型与溯河洄游型种群间、高纬度与低纬度种群间，以及波罗的海种群与其他所有种群的对比中。最后，本研究探讨了该SNP芯片在未来物种保护、资源管理及水产养殖领域的潜在应用方向。